Acting-Commander Traynor
by l OmegaInfinity l
Summary: Post ME3/The Reapers are dead. The war is over. But enemies remain. Except now, Shepard is stranded on Earth, and the Normandy is left without a Commander, with no idea that she's alive. And to make matters worse, no sooner did the Reaper threat end then Cerberus jumped in to pick up the scraps. Without Shepard, who's left to take charge? The one closest to Shepard. Naturally.
1. Chapter 1: One War Ends

**A/n: Okay, real quick before we get started:**

**My Shepperd: **

**First name: Crystal**

**Female**

**Pale skin**

**Short, silver hair**

**Piercing golden eyes**

**Romanced Traynor. Obviously.**

**As everyone who ever played these games know, everyone makes different choices. And trying to explain every choice I made would take up an entire chapter all it's own. So, I leave it to you, the reader, to piece it together yourselves. That okay?**

**On we go!**

* * *

**Chapter 1: One War Ends...**

**Five Hours After The War**

The Reapers are dead.

Throughout the galaxy, reality is only just sinking in. On every colonized planet, on every Allied ship, people of all species release cries of triumph as their scanners register no sign of the Reapers, each celebrating in their own way. From the Turian forces on Palaven to the Asari Commandos of Thessia, from the ruins of Tuchanka to the Quarian fleets, the sense of victory is universal.

Except for on one ship.

On an uncharted jungle world lay the _SSV Normandy_. Inside her, her crew rushes from deck to deck, making the last minute repairs needed to get off world.

As they work, however, they make sure to steer clear of the port-side observation deck, who's door hadn't been opened as a sign of respect for those within.

Inside, gathered around the poker table, sat a solemn, mismatched group of eight: a muscled man with a mohawk, his grey armor dented, even shattered in some places. A human Spectre, her blue battle suit in as bad, if not worse shape. An Asari Shadow Broker, head in her hands, arms resting on the table. A dark-skinned shuttle pilot, an untouched shot glass held between loose fingers. Another pilot, leaned far back in his seat, the look of frailty about him having nothing to do with Vrolik's Syndrome. A battle-scared Turian supporting a female Quarian leaning against him, unseen tears falling behind her visor. And rounding the table...

...a very distraught Comm Specialist.

Though no sound escaped her, her pain was the most obvious to everyone else around the table. Though none could blame her, all were surprised, simply due to the revelation of exactly what she was to...

...to...

* * *

**Six Hours Ago**

"_Normandy_! Do you copy?"

Samantha froze. All throughout the hell that is the Battle for Earth, she had been working franticly at her post, sifting through the constant bombardment of radio traffic, trying to separate key information from combination of commanding orders, status updates, and pleas for assistance that streamed from the ruins that were once London. While she usually would relish from such a challenge, the knowledge that her job largely contributed to whether soldiers on the battlefield lived or fell to the Reapers was wearing her nerves thin. Especially the thought of one particular solider, one who was currently on the equivalent of a suicide mission.

The same one who's voice now streamed from from her console, the normally secure comm channel found completely by accident.

"I need an evac. Right now!"

Samantha ceased all movement, an instant backlog of messages and comm chatter cluttering up her terminal. She could still hear the conversation clear as day.

"We're taking heavy losses up here, Commander." Joker's voice answered. Then Samantha felt the _Normandy_ dip and turn, the amount of enemy fire against the hull increasing. A few moments latter, Joker replied, determined. "On our way, Commander."

Samantha stood frozen for a moment as the ship continued down. A few members of the crew were starting to note her lack of activity as the _Normandy_ landed, wondering is she had maybe cracked under all the pressure.

As the faint hint of a hiss sounded throughout the ship, signaling the ramp lowering, Samantha bolted. As if in a daze, she suddenly found herself in the elevator, the door closing on the shocked look on the officers she blew past. A small light along the top of the car showed her passing the crew's quarters... Engineering...

The Shuttle Bay.

As the doors opened, Specialist Traynor was met... with hell.

Looking out of the _Normandy_, Samantha's eyes were instantly drawn to the massive pillar of light in the distance, then to the just-as-massive Reaper known as Harbinger. A glowing red dot near it's center signaled that it was charging for an attack. Fear froze Samantha to the spot, fully aware of the devastation that was about to be wrought. At the last minute, a large flash of laser fire crashed into Harbinger's side, likely a lucky pot shot from one of the thousands of ships waging war in orbit. Harbinger barely staggered, but turned it's red charge in the offending direction and opened fire, releasing it's own beam of red energy. All this in the span of a second.

Samantha's gaze was torn from the massive behemoth by a voice at the bottom of ramp:

"Damn it, I can do this."

Her eyes were instantly drawn to the unfolding scene.

James Vega, signs of fatigue obvious, stood there supporting a beaten, bloody, and frustrated Lieutenant Commander Williams. Garrus Vakarian lay cover fire for the soldiers retreating up the ramp. And in the center of it all...

Shepard.

The proud Commander still stood tall. Her jet black armor scratched and painted in Reaper blood. The tactical visor that usually covered her golden eyes was shattered, jagged orange shards jutting out from the headpiece where glass once was. Seeing the fire in her eyes still there despite it all made Samantha's heart soar.

It was her next words, however, that made the Comm Specialist's blood run cold.

The proud facade crumbled for a brief moment, reveling a look of desperation all too human on the woman's face. She looked into Ashley's eyes and said, in barely a whisper, "I need to know somebody's getting out of this alive."

Ashley was left at a loss for words as James tried to pull her up the ramp. Shepard turned from them, looking back towards the beam. Harbinger stood behind it, still firing at a growing fireball of in the distance. It looked like Shepard had every intention of running off right then.

Someone stopped her.

"Shepard!"

The Commander stopped all motion. Her shoulders seemed to slump as she turned around, a sad smile on her face.

"Sam..."

Samantha Traynor stood halfway down the ramp, surprising the other three war heroes. If the Comm Specialist noticed, she didn't show it. Her eyes were only focused on one thing.

The Commander.

_Her_ Commander.

"Don't do this," She pleaded, her voice barely audible above the sounds of war around them. "Please. Let someone else be the hero. Don't do this."

Shepard looked up at her, the pain in her eyes having nothing to do with any physical injury. "It's gotta be me, Sam. I always knew that."

Tears now escaped from Traynor's eyes as her reality seemed to be crashing around her. "I..."

Shepard, seeing this, made her way up the ramp to meet her. "No matter what happens here today," she declared, putting a hand to Samantha's cheek, wiping away a tear. "I'll always love you. Never forget that."

Samantha could feel her heart breaking. Shepard, the woman she loved, was basically telling her that she was going to die.

Several thoughts crossed her mind. She could plead further for Shepard not to go. She could break down in a fit of hysterics. She could even do something crazy, something guaranteed to get her court-martialed.

But she didn't do that. Instead, she stood as tall and strong as she could, and looked deep into the Commander's eyes. "Promise me something."

Shepard's eyes turned even more pained. "Sam..."

"Crystal." The use of her first name silenced the Commander. Samantha continued. "Just promise me... if there's any way to come back to me, no matter how crazy..." Her voice started to crack on the last three words. "...please take it."

Shepard's eyes widened, but then sharpened. She gave a sharp nod, a determined smile on her lips. "You can count on it."

Samantha nodded back. Then, in a whisper that only those near could hear, she vowed, "I love you too. Always will."

Shepard smiled. Lowering her hand from Samantha's face she started backing down the ramp. A massive roar echoed across the landscape, causing everyone to look up.

Harbinger started to turn back towards the _Normandy_. Miles away, the fireball that once was a Turian Cruiser fell towards the earth, likely about to take a large section of London with it.

Shepard looked over at James and Ashley, who, until Harbinger's roar, had been watching the scene in silent shock. "You two get aboard."

James gave a sharp nod and started pulling Ashley up the ramp. Ashley pulled against him, wincing as fresh blood ran from her wounds. "Shepard..."

The Commander gave her a soft smile. "Take care of yourself, Ash."

Ashley was silent for a second, before nodding. James gave Shepard a halfhearted smirk. "Good luck, Lola."

Shepard's smile widened slightly. "You too, James. Now, go!" With only another nod, James and Ashley started limping back up the ramp.

Shepard spared a quick, heartfelt look into Samantha's eyes before turning to her Turian friend, still blasting at the Husks trying to claw their way to the ship. "Garrus, get her on board. Keep her safe."

The battle hardened Turin nodded sharply. "Yes ma'am. And Shepard?" Garrus gave her the Turian equivalent of a smirk. "Stay alive." Before she could respond, he started back up the ramp towards Traynor, who stood stock still halfway down the ramp.

Shepard gave a quick glance over her shoulder, back towards the beam. She started backing away from the ship. She gave Traynor one last look. "Go!" She ordered. And then she turned...

And charged back towards the Reapers.

Samantha felt the powerful urge to run after her. Before she could act on it, she felt a claw-like hand on her shoulder. She turned to see Garrus right beside her.

"Traynor, we need to go!"

Samantha looked at him. Then she turned away from the battlefield. She felt the jolt as the ramp started to close and the _Normandy_ took off.

Leaving the love of her life behind.

* * *

**Present**

The silence stretched around the table, as it had for the last hour. Ever since entering the room, no one could think of what to say. So they stayed silent, simply taking comfort in each other's presence.

"We should have stayed."

The group turned to speaker, all except for Traynor, who kept staring at her hands.

"And done what, Joker?" Garrus asked. His tone wasn't angry, more tired, like the same thought had crossed his mind already. "We had our orders." He let out a sad sigh, wrapping his arm a bit tighter around Tali. "Besides, we all saw the feed. Where she was at, none of us could have helped her."

_The feed, _Traynor thought absently.

* * *

After being knocked off course by that red pulse, Joker was forced to set down on the nearest planet with a breathable atmosphere. Half the ships systems were fried, including the subspace messengers. Traynor worked in a daze while she repaired them, ignoring the occasional look from various crew members. When she did after two hours of work, she quickly wished she hadn't.

Upon activation, a large file appeared, labeled from Admiral Hackett to the crew of the _Normandy_. Attached was a short message:

_To the crew of the _SSV Normandy_,_

_We have just begun contacting planets around the galaxy. While we are hesitant to make the assumption that the Reaper threat is now over, it is starting to appear so. We have received word that all Reaper activity has dropped to zero on Earth, Palaven, Thessia, Tuchanka, Sur'Kesh, and Rannoch, just to name a few. It would seem that Project Crucible is a success. From the reports, it appears that every Mass Relay throughout the Milky Way has been has been put out of commission by the Crucible's energy wave. However, the damage is reparable. Early estimates expect the major Relay lines will be operational within four months, with all Relays repaired within a year. _

_However, there is unfortunate news. After the Crucible was activated, the Citadel was heavily damaged. While most civilians had been evacuated before moving it towards Earth, it would appear that the majority of officers stationed in the first sector perished during the battle. However, early investigators have discovered something peculiar. While all unneeded power was thought to have been shut off during transit, it appears that the security cameras on board the Citadel remained active. What it captured was... There is no easy way to say it. We believe that the Citadel security system captured the last moments of Commander Crystal Shepard. While we have not yet found a body, the evidence is very staggering. As the _Normandy_ was her ship, we felt it was only right that it's crew should be the first to see the footage before it is released to the public..._

The message went on from there with apologize to the crew for their loss, but Traynor didn't get that far. As the Comm Specialist, she was the first person to read the note. It wasn't until she let out a strangled cry of inner pain, breaking down right there at her console, that the file was made aware to the rest of the crew.

Surprisingly, Tali was the first one at her side. After reading the note herself, the Quarian did her best to calm the grief-stricken Traynor, while fighting off her own grief at the loss of one of her closest friends.

Word quickly spread throughout the ship about the message. As Traynor was in no shape to do much of anything, Tali was the one to activate the video, projecting it across every working vid-screen on the ship. The crew watched as Shepard, bruised and bloodied, entered the Citadel. They witnessed the confrontation between Shepard, Anderson, and the heavily indoctrinated Illusive Man. By this point, the crew closest to Shepard had found there way to the CIC. As the Illusive Man took his own life, Traynor heard a bandaged Ashley of to her side mutter, "Serves the bastard right."

The crew watched as Anderson slipped into the void as Shepard made her way up, cradling the bullet wound in her side. The crew was silent as Shepard was confronted with the Catalyst, all listening intently as it explained its purpose, what it was, what the Reapers were. And then, it presented Shepard with a choice. She could choose to Destroy, not only the Reapers, but all synthetics, wiping them from the face of the galaxy. She could Control the Reapers, doing what the Illusive Man couldn't, using the Reapers as a tool to better the universe. Or, she could Synthesize new DNA for the entire galaxy, blurring the line between organic and synthetic, thus rendering the Reapers obsolete.

The crew watched as Shepard contemplated each choice, giving all of them an honest thought. Then, in the words of James Vega, she chose to 'blow them all to hell.'

Shepard puled her pistol, and limped towards the red device. She fired a few rounds, breaking the glass covering. As she neared it, her resolve seemed to grow, her limp disappearing. As she unloaded her weapon into the machine, fire and red bolts of electricity shot out. Finally she found herself right in front of it, an inferno blazing inside the unstable machine. Shepard saw this, a sad smile forming on her lips. The Commander closed her eyes and said, in a clear, strong voice...

"I'm sorry, Sam."

A red flash. A human form flung offscreen. Then, static.

* * *

Traynor hadn't spoken since the video ended. She had just stared at the static on the screen. When James had suggested that the Commander's friends gather on the observation deck for a drink, Tali had had to lead her there, at which point she simply had kept here head down, tears flowing silently.

"I still think we could have done something." Joker mumbled dejectedly. It was clear that he knew he was wrong. They were just words.

Tali gave a small sniffle, before pushing lightly on Garrus. The Turian released his grip on her, his now free arm going for the shot glass in front of him. The Quarian gave a sidelong look at Traynor, still in her trance. She reached over and put a hand on her shoulder. "Ms. Samantha? Are you okay?"

Traynor looked up at the touch, gazing at the blue orbs behind the Quarian's visor. At first she didn't seem to register Tali being right in front of her. Then she gave a quick shake of her head, her eyes blinking rapidly. "Oh... oh, I'm... I'm okay, Tali." She sounded like she had just come out of a daze.

Tali wasn't convinced. "Are you sure?"

Samantha took a deep breath. "Yeah. Yes, I'm... I'm okay. It's just..." The Comm Specialist had to clear her throat to keep from choking on tears. "I'm just really going to miss her."

Tali let out a sigh, patting Samantha's back as fresh tears fell down. "We all will. She was a loyal friend."

"She was one hell of a solider," Garrus stated, swallowing another shot of Turian ale.

"Never gave in," James agreed, doing the same.

"Brave to a fault," Ashley added in.

"She never left anyone behind," Liara claimed, finally pulling her head from her hands. "Not if she could help it."

"Always making sure we were okay." Cortez affirmed. "Always looking out for us."

"She had good sense of humor." Joker chimed in. "Always admired her for that."

Samantha felt a small smile form. The pain was still there, glaringly so, but, at the moment, surrounded by people that felt the same way, the pain seemed numbed.

The stiffness that had dominated the room had dissipated. The silence was now more comfortable, friendly.

Suddenly, James broke the silence. "So, uh, Traynor," he started awkwardly. Thinking back, he couldn't recall ever saying two words to the dark-skinned woman. Samantha turned to him. James rubbed the back of his neck, suddenly uncomfortable. "You and the Commander..."

"James!" Ashley exclaimed harshly, elbowing the large man in the ribs.

If he felt anything from the blow, he didn't show it. "What? Look, I am sorry, but I know I'm not the only one wondering."

Though they were giving him dirty looks, several people around the table secretly agreed with him.

"That still doesn't mean you should-"

"Ashley." All attention at the table was focused on Samantha. Her tears had finally stopped falling, a bit of shine in her eyes. "It's okay." Ashley gave her a long look before accepting her words. Samantha then turned towards James. "And yes, James. Me and Shepard ar- _were_ together."

James, catching her minor slip up, simply nodded and let the mater drop. Garrus, however, let out a small chuckle.

Joker raised an eyebrow at him. "Something funny, Scarface?"

Garrus gave another chuckle. "Just thinking on how we were all so close to Shepard, yet none of us could tell she was in a relationship. Though, thinking back, she did seem to smile a bit more the past few weeks."

Joker opened his mouth to say something, but was cut off by a voice from the comm system.

"I knew."

Everybody looked up in shock, save for Joker, who was trying not to laugh.

"EDI!?" Tali exclaimed, baffled.

"Yes?"

"B-Bu-bu-but-but-" Samantha stammered as she stared up at the speaker EDI's voice came. "How?"

"I assume you are inquiring how I survived the Crucible pulse? It was quite simple. As the _Normandy_ tried to escape from the pulse, I ran a scan on it. The pulse targeted VI and AI platforms and programs, so I made myself something else."

"Excuse me?" Ashley asked, perplexed.

"I broke my AI software into four-thousand, six-hundred and eighty-four individual programs and scattered them thought different systems on the ship, thereby having no resemblance to an AI. I also created a program that would activate one hour after creation that would, as Jeff put it, 'pull myself together.'"

Everyone stared up at the speakers for a few moments. Then James through up his hands. "I'll buy it!"

This got a light bit of laughter from everyone. Cortez turned to Joker. "You know she was going to do this?"

Joker scoffed. "Would have been nice to know, wouldn't it? No, after that pulse passed us, I spent an entire hour trying to figure out were she was. Turns out the pulse vaporized her body. I was about to break down when I hear her voice coming out of the speakers."

After a minute, James put a hand to his temple. "This day has been too friggin' long."

Murmurs of agreement sounded from everybody. Garrus looked around the table before speaking. "Your right, James. I think I speak for all of us when I say that this has been one of, if not _the_ most trying day of our lives. So I say we finally let it end and get some sleep." There were nods all around the table. Garrus nodded with them. "Right. But first things first: EDI?"

"Yes?"

"Do you have any idea what sector we are in?"

"Just a moment." Edi was silent for a full two seconds. Then: "Scanning complete. We appear to be in the Petra Nebula, two-hundred and nineteen light years from the nearest Mass Relay."

Garrus thought for a moment. "From what we heard from Admiral Hackett, the Relays are dead. But... if memory serves me right, Planet Elysium is in that same system, right?"

"That is correct, Garrus."

"Okay." He then turned to the other seven people in the room. "The fact remains that right now, we don't have a commanding officer." He sparred a quick glance at Samantha, who's head dipped down for a moment, before nodding for him to continue. "Also, the QEC is down and we don't have the materials to repair it. However, there is an Alliance base on Elysium that likely has a working one. I say that we go there and contact high command. Anyone think differently?"

No one did. Seeing this, Garrus nodded. "Okay. Joker, think you can set the autopilot before you retire?"

Joker grunted as he carefully pushed himself away from the table. "I usually sleep in my chair anyway. I'll get us there."

Garrus smirked. "Good man. Alright people, let's go put this day behind us."

More murmurs of acknowledgment sounded from around the room as the group rose to their feet. As they exited the room, everyone went their separate ways. Joker was already headed towards the bridge in the elevator. Liara headed off towards her room along the port side. Garrus went back to the main battery, to do what, no one knew. James and Ashley waited for the elevator with Cortez, most likely to deposit their armor.

As Samantha walked out of the room, she felt Tali put a hand on her shoulder again. "Your sure your okay, Ms. Samantha?"

Samantha gave her a smile, small, but genuine. "I'm fine, Tali. It hurts, but... I'll be okay." She gave the Quarian a small chuckle. "And please just call me Sam. All my friends do."

Somehow, Samantha could feel Tali smile behind her mask. "Okay. I'll see you tomorrow." She then headed off towards the main battery after Garrus.

Samantha smiled as she watched her go. When she disappeared around the corner, however, the Comm Specialist felt very alone. The others had already disappeared down the elevator, headed towards the shuttle bay. Samantha turned to walk towards the crew quarters, but stopped. She looked towards the elevator, contemplating. With a sharp nod, she walked over and called for it. When the door slid open, she stepped inside.

"Deck one." She called out loud.

The car gave a small jerk as it started it's ascent. After a few seconds, the door opened to reveal the small compartment right before the captain's quarters. She walked up to the door. She typed a quick command on her Omni-tool and the door unlocked.

She stepped inside and was greeted with memories. While they had only been together for a few months, Samantha and the Commander had spent almost all of their seldom offtime up here, together. Whether they played chess, talked, or simply enjoyed being near each other, they always were happy because there were together.

And now she was gone.

Samantha's gaze drifted across the room. From the tiny model ships in the display case to the cascade of color that made up the aquarium, even to the small closet off to the side of the bed; all of it reminder her of Shepard.

She made her way silently to the bed. She pulled off her uniform leaving her in her underclothes. As she crawled under the covers, she was distinctly aware of how... _empty_ it felt.

As Samantha started to slip into the darkness of sleep, tears once again began to fall. But at the same time, she felt something. Something that wouldn't let her fall into the bleak depression she had been in earlier. It almost felt like... like she knew.

That somehow she knew...

* * *

**Earth**

_...that she was still out there._

The city of London, now a shell of it's former self. Buildings demolished. Wreckage everywhere. The corpses of soldiers from varying species lay strewn across the ground. And yet, no one is sad. For there is one new feature in this shell of a city that makes the spirits of all Allied soldiers soar:

The massive corpse of Harbinger.

The sight of the original Reaper now dead stands as a testament to what has been accomplished: the entire galaxy united to stop a common foe. And now is the time to rebuild.

As the sun starts to rise on the decimated London skyline, Allied troops march up and down the streets, searching for survivors as well as wounded soldiers. Their search has not yet reached the most devastated part of the city.

A large structure stands in a crater, high above the rubble. In it's center is a massive beam of light, stretching all the way into the heavens. At the foot of this structure lay dozens of bodies, all of which men and women who died in a made scramble to reach the beam.

Among them, laying in the rubble, is a figure wearing ruined armor. Armor that bares the symbol 'N7.'

(gasp!)

**A/n: As you might have guessed, this is my first Mass Effect story. Hopefully I did a good job. If you liked it, please tell me so I now to continue. No reviews equal no story.**


	2. Chapter 2: Another Beguins

**Chapter 2: ...Another Begins**

**Seven Hours Later.**

"Jeff."

The bridge was shroud in darkness, the only light coming from a few activated panels. Stars sped passed the windows, millions of twinkling lights against the black backdrop of space. Joker lay reclined in his chair, sounds that could only be compared to active energy saw coming from his mouth.

"Jeff?" EDI asked over the comm systems.

Joker shifted a bit in his sleep, his head rolling to the other side of the chair. A shockingly human-like sigh sounded over the speakers.

"JEFF!"

"Ah!" Joker almost fell out of his chair. His hand practically slammed into his forehead in a quick salute. "Lieutenant Jeff Moreau reporting for duty, sir!" An instant later, his other hand went to his now throbbing shoulder. He looked around in confusion for a moment, before staring up at the ceiling, struggling not to scowl. "EDI, please never wake me up like that again. Makes me think I'm back in flight school."

"I'm sorry, Jeff." EDI apologized. "It was not my intention to elicit such a reaction from you." Then, a surprisingly soft tone entered the AI's voice. "Are you okay?"

Joker looked up and smiled, carefully flexing the pained appendage. "I'm fine, EDI. Nothing's broken." He started going over the sensors of the ship, making sure nothing had happened while he slept. "So, any particular reason you woke me up, or did you just miss the sound of my voice?"

"Long range sensors have picked up a distress signal from a Turian cruiser. They claim that their ship is inoperable due to the loss of their VI." (pause) "Although, I do find your vocal patterns... pleasing."

Joker hands stopped moving for a moment. Then he let out a light chuckle. Instinctively he reached to call the captain's quarters. Then he froze, his hand hovering over the comm systems. "Um... EDI?" He asked uncertainly. "Who do I call?"

EDI was silent for a few seconds. Then she answered, "As it is a Turian craft, perhaps Garrus would have some insight on the situation?"

Joker nodded. "Sounds good." He typed a few lines of code into the displays. "Garrus?" He called into the comm.

"What do you need, Joker?"

"We've got a Turian Cruiser sending us a distress signal. Think you can come up here and give me a hand?"

"I'll be right there."

Five minutes later, the door to the bridge opened, Garrus walking in.

"Were are now in visual range." EDI announced. A vid-screen opened up in front of Joker

"Doesn't look like any Turian Cruiser I've ever seen," The pilot commented, staring at the screen. "And I've seen a lot."

The ship was shaped like a Turian cruiser, but was jet black, and significantly smaller. Deep blue lights glittered across it's hull.

"It's one of the new _Shadow-_class cruisers." Garrus explained. "Fast, stealthy, and armed to the teeth. Mostly used for recon or hit-and-run tactics. Maximum crew of twenty. Though no one will admit it, I believe it's my military's answer to the _Normandy._" He put a hand to his chin in thought. "Though why one would be all the way out here escapes me."

"Then let's find out." Joker said with a smirk. We worked at the controls for a minute before speaking into the comm. "Turian Cruiser, this is the Normandy. Please state you're the reason for your presence in this sector."

In answer, a line of text scrolled across the screen.

"Says they were stationed here to monitor the Reaper occupation of the Vetus system." Joker read.

Garrus nodded. "Makes sense. Elysium, Sidon, Grissom Academy; there's a lot of Alliance tech in that system. High command would probably want to know what the Reapers were doing with it."

"Hmm..." Joker thought for a moment. "EDI, anything suspicious about the signal?"

"Nothing that I can detect, Jeff. Everything about it seems legitimate."

Joker turned his chair around to Garrus, a questioning look on his face. Garrus contemplated for a minute, then looked Joker in the eyes, and nodded an affirmative. Nodding back, Joker turned back to the comm. "Turian Cruiser, we'd be more then happy to help. Prepare for docking."

* * *

A few minutes later found Garrus standing outside the airlock, waiting to greet his fellow Turians as the ships docked. He glanced towards the CIC, the four officers that made up the night shift milling around, keeping the ship running.

A faint hiss drew his attention back to airlock. The tell-tale beeping of a door opening sounded, telling that the visitors now stood in airlock itself.

Garrus tapped on the green holopad, and the doors slid open to reveal six figures in armor.

White and yellow armor.

"Oh crap."

* * *

"...lert! I repeat, Red Alert! The ship is under att-SSSSCCCCHHH..."

Samantha jolted awake as Joker's voice was drowned out by static, before the comm went silent.

Looking wildly around the room, a sense of dread quickly filled her. The room was bathed in a pulsating red light, constantly glowing on and off. A sound like hail falling echoed through the bulkheads.

Samantha threw off the covers. The Normandy was under attack, and she needed to be at her post. She jumped out of the bed, reaching for her uniform laid over the sofa.

(Boom! Boom!)

Samantha froze as two heavy blows hit the door to the room. A third sounded. Muffled voices could be heard outside. She couldn't make out what they we saying, but they sounded male. And angry.

Samantha cautiously climbed the short flight of stairs that split the room in half. She edged towards the door, for the red holopad on its front. A quick tap would show her who was on the other side via security cam. She had just reached out her hand, when...

(csh-csh-csh-csh-csh-csh-csh!)

The Comm Specialist dived around the corner, slamming her back against the bathroom door.

Someone was shooting at the door!

The noise persisted nonstop for three seconds as the attacker apparently an entire thermal clip into the door, to no effect. As the gunfire ended, the voices began again, even angrier then before.

Samantha's mind was in a paradox, both moving a mile a minute and completely stalling. She'd never been in combat. She'd gotten into the Alliance navy thanks to her mind, not her ability on the battlefield. Hell, she never even _fired_ a gun before outside of basic training. She had one of the rare jobs that existed that was both extremely important and relatively "safe". Aside from the _Normandy's_ space assaults, she'd never seen battle.

And now someone was trying to kill her.

She tried to calm herself, to slow her mind. She closed her eyes and focused. She thought back to Basic, to the lessons her instructor pounded into her. She searched her memory, looking for the moment she needed.

_Okay...okay...it was... it was my second year... third week... Tuesday... no! Thursday. Yes... Thursday... Commander Litchfield's class... the lesson... lesson was... survival. Yes! Separation and Survival Training!_

Samantha's eyes snapped open as the face of her former Commander materialized in her mind: a gruff, war hardened man, a scar going over milky, dead left eye. A man who didn't care whether you were technical prodigy or infantry grunt. Rich, poor, strong, weak; didn't matter. All he cared about were two things: if you followed orders, and how well you followed them.

She listened as his voice played in her mind:

"_In the event you find yourself cut off from command, you have only two objectives: Number one should go without saying: survive. Number two: Unless your mission says otherwise, reestablish contact, by any means necessary short of inciting an interplanetary indecent."_

Samantha released an unneeded small sigh of relief. It was by no means a solution, but it was a step in the right direction. As the voices outside the room continued to converse, Samantha slid into the desk side chair below the model ships. She tapped the terminal and brought up the comm.

=ACCSESS DENIED=

Samantha frowned. That... shouldn't be possible. This was Shepard's personal terminal. It had access to every other computer on the ship, capable of overriding any security, with EDI''s help, of course. The only way it couldn't be accessed was if...

If the entire comm system was being blocked.

Samantha felt the strategist in her take over. _Okay, hypothetical situation: you want to invade the _Normandy_. Best course of action? Divide the crew. Best way to do that? Disable the comms. _

She remembered Joker's brief attempt at a warning, how it was cut off by static.

A few more taps brought her too a screen filled with lines of code. To the average person, it was just a jumble of numbers, but to her, it was like having the enemies playbook right in front of her.

. _Let's see... class two dampening field... level three encrypted firewall... _Her eyes widened. She recognized these programs. She'd dealt with them before.

Cerberus.

Samantha quickly squashed the flood of questions that filled her mind. Getting worked up wouldn't help her. Her fingers quickly glided across the terminal, attempting to break through the binds Cerberus had placed on the ship.

As she worked, she was aware that the voices (who she now assumed were Cerberus agents) had fallen silent. A faint hiss could be heard instead. After a moment, she placed the sound: an engineer's torch.

They were cutting through.

The screen suddenly went green. A small smirk formed on her face. She was in. _Traynor: one, _she thought._ Cerberus: zero._

Whoever, know she had a dilemma: who to call? For all she knew, everyone else on the ship was captured, or worse.

Samantha felt a light bulb go off in her head. There was one person she was sure she could reach. She pressed on the 'call' button. "EDI? Can you hear me?"

Seconds ticked by. One... two... "Hello, Specialist Traynor."

A sigh of relief escaped her. "Oh, thank God. EDI, what the hell is going on?"

The AI's voice seemed to be it's usual neutral tone, but Samantha caught a minuscule amount of strain in it. "Cerberus troopers have laid siege to the Normandy."

Even though she'd already guessed as much, a cold chill ran through the Specialist at the confirmation. "How did this happen?"

"We encountered a disabled Turian cruiser, claiming that, with their VI having been destroyed, most of their systems were down. The communication seemed legitimate."

Samantha thought for a moment. "They probably learned from their mistake at Grissom Academy." She muttered, mostly to herself. Out of habit, she looked towards the speaker EDI's voice came from. "What happened next?"

"We docked with the ship. Garrus opened the hatch, expecting to be greeted with Turian soldiers. Instead, six Cerberus Assault Troopers opened fire."

Dread seeped into Samantha. "Is he...?" She trailed off.

"He is alive, but injured. He was shot in the shoulder before retreating to the bridge. He and Joker have locked down the bridge with themselves inside."

"What about the rest of the ship?"

"That information is... limited." Samantha could hear what passed for frustration in the AI's voice. "When Cerberus entered the ship, they opened fire on the CIC. There were... casualties." The dark-skinned woman tensed. She was friends with most of the CIC officers. "The survivors retreated to the War Room, locking it down. After that, Cerberus... _suppressed_ me."

Before Samantha could ask her to elaborate, a sharp hiss filled the room. Looking behind her, Samantha saw the white-hot tip of laser torch jutting out from the top of the doors, sparks flying as it inched down the door agonizingly slow. A cold sweat ran down Samantha's spine at the sight.

The sound did not go unnoticed by EDI. "Specialist Traynor, what is that noise? What is you situation?"

The Specialist forced herself to tear her eyes away from shower of sparks. She tried to let out a slow, calming breath, but it came out short and choppy. "Someone's cutting their way into the room."

EDI was silent for only a moment, but that moment seemed to stretch for hours. When she spoke, it was not in the light, inquiring voice that she usually used. It was the cool clipped tones of solider. "Specialist, I trust you know how to use a weapon?"

Samantha was surprised by the sudden question. "Y-Yes, but-"

"Go to the left-side table by Commander Shepard's bed." EDI cut her off. "There is a weapon hidden between the bed and the table."

Despite herself, the dark-skinned woman couldn't help but ask, "How did-?"

"I am the AI of the _Normandy_." She was once again cut off, but she could hear a bit of what passed for pride in EDI's voice. "As such, it is in my programing to keep track of all equipment on the ship, including weapons, both in and outside of the Shuttle Bay. Therefore, it is part of my knowledge that Commander Shepard kept a Class Ten Scorpion pistol at her bedside, 'just in case,' as she put it."

Snapping out of her daze at this new revelation, Samantha did as she was told, practically running passed the sparks that cascaded down the door. Sure enough, nestled between the bed and the desk side table was the shape of a weapon. Samantha pulled it out, surprised by how unexpectedly heavy it was. It was alien in design, white, all curves, and with a grip that obviously had not been designed with humans in mind. Despite that, she was able to hold it with a strong, if uncomfortable, grip.

Normally, Samantha would have laughed, saying that Shepard was too paranoid.

Now she wondered if maybe she was too naïve.

Her thoughts were broken by EDI's voice. "Specialist, have you found the weapon?"

"Y-Yes, I have EDI." Samantha answered, holding the gun awkwardly in her hands.

"Good. Now, take cover behind the stairs."

In a strange daze, (she would later realize that she was in shock of the situation) the Specialist put her back to the directed wall. Peeking around the corner, she had a clear shot at the door, which by now was cut halfway down its length. The red holopad fizzed and bent like static as the torch cut through the sensitive circuitry.

"Samantha," EDI's voice calm, yet strained. "You are going to have to trust me. I will walk you through this conflict. Do you understand?"

The Specialist fought down the sudden waves of nausea and doubt, trying to recall every minuscule amount of combat training she'd learned in Basic. She let out a shaky breath. "Y-Yes, EDI. I understand."

"Confirmed. Aim your weapon at the cutting tool."

She did, ignoring how the sights of the pistol shook as she looked down them.

EDI continued. "I now have limited control of the captain's cabin. I shall count to three. On the third count, I will open the doors. Specialist Traynor, the instant the doors start to open, **squeeze the trigger**. You must not hesitate. Understood?"

"Understood." The word was out of her mouth before the thought had been fully processed.

"Okay." Was it her imagination, or did the AI seem... worried? "One..."

Samantha sucked in a deep breath.

"Two..."

She placed a slender finger on the trigger.

"Three."

The doors slid open...

(Cshoo!)

The Cerberus Engineer jerked in surprise as a vibrating blue orb latched onto his hand. The Assault Trooper next to him was startled by both the doors sudden opening and his companion's unexpected reaction. Looking into the room, all he saw was a clearly terrified woman, clad only in her sleepwear, clutching some type of weapon in an inexperienced grip. Instinctively, he raised his rifle and took aim.

Samantha's heart completely stopped as the Assault Trooper put her in his crosshairs. The Engineer beside him had recovered and reached for his own weapon, seemingly oblivious of the orb on his hand.

Samantha froze, her eyes wide. She could actually see the man's finger squeeze the trigger...

A deafening explosion rocked the confined space. Horror gripped the Specialist as the two men in front of her were reduced to twin eruptions of blood and muscle. The destruction was so complete that not even bone were left, just a fine white powder that mixed with the gore.

The sound died down, a crushing silence in its place. Seconds ticked by. Over the Comms, EDI started asking questions. "Specialist, are you unharmed? Are the Cerberus agents dealt with?"

The silence was broken by the sudden sound of the Scorpion pistol clattered to the ground.

_I just killed someone._ This thought replayed in the Comm Specialist's head as if on a loop. Her unblinking eyes remained glued to the pile of gore that now painted the walls and floor just outside the room._ I pulled the trigger and now their dead. Just like that. _Her breathing started to increase, becoming faster, choppy, uneven. _I just-_

"Ow!" Samantha's mind was put back in place by a large electric shock to her left hand. As she cradled it, she saw that her Omni-tool hand was partly activated form of some unfamiliar tool. After a moment, she recognized it as a taser.

"Samantha." EDI's voice was more urgent now. "Are you okay?"

Samantha looked between the comm and her Omni-tool, piecing together what had happened. She took a deep breath through her mouth and let it out shakily. "Yes, EDI. I'm fine. Thank you."

"Good. I apologize for the shock."

"No, don't. I..." her eyes flicked back to what was left of the Cerberus agents. The blood was starting to seep through the grating on the floor, running into the ships inner workings. She forced her eyes from it. "I needed it."

EDI was silent. Then; "Specialist, I need to be frank with you."

Samantha blinked, unsuspecting the statement. "O...kay?"

EDI wasted no time. "Specialist, the Normandy is under siege. As I am locked out of most systems, we have no way to make contact with the rest of the ship. The only reason you managed to contact me is because I essentially _am_ the communications network."

That left Samantha a bit disheartened, and more then a little hopeless. "Then what do we do?"

"When Cerberus came aboard, they did two things: They shut down the communications systems, and disabled the automated defenses." Samantha didn't say anything, so she continued. "If someone could reach engineering through the maintenance shafts undetected, then, with my help, they could reactivate the automated defenses manually."

Samantha nodded. It made sense. If the defenses were back online, then Cerberus would have to fight the ship itself. But who would they get to...

Her mind stalled.

"Oh no. No. No! EDI, you can't seriously expect me to-"

"It's only with my help that someone could bypass security to activate the defenses. You are the only member of the crew I can contact. In addition, you have experience with disabling Cerberus programing. It's only logical that you be the one."

Logical. Samantha suddenly had a strong hatred for the word. "EDI, I'm a Communications Specialist, not a solider!"

"As you a member of the Alliance Navy, that statement is technically inaccurate."

"Ugh!" Samantha sunk into desk-side chair, putting her head in her hands. She knew she was going to lose this argument. In desperation she whispered, "EDI, I can't do this. I'm just one person."

EDI was quiet for only a moment. When she spoke, her voice was the kindest Samantha had ever heard from her.

"Commander Shepard was only one person."

Samantha was silent, EDI's words rolling around in her head. _It wasn't the same! Shepard was...Shepard. She was strong; she was brave. She was trained in combat, had seen dozens of battlefields. She was a tactical genius. She was..._

Human.

That was the thought that stopped Samantha cold. Despite everything she'd been through, despite all the training, all the heroics, every single unbelievable victory, one thing was true: Shepard was still human. It was this fact that had surprised Samantha early on in their relationship. That under all the armor and scars, there was a person that remained hidden, a person that Samantha was likely the only one to ever see: A human woman. A woman who still hurt. Who still cried. Who still feared.

Samantha remembered Shepard's nightmares. The Commander would never tell her what they were, but she could tell that Shepard was hurting. One night Samantha had woken up in the dead of night to find tears streaming down her lovers sleeping face.

It was that moment when Samantha had her realization: Shepard wasn't some superhero like some people made her out to be. She was just a normal person, who happened to be thrown into a world of pain and death, and managed to survive.

And if one normal person could do it, so could another.

By this point, Traynor had back slipped into her uniform. As she walked back the comms desk, she scooped up the Scorpion pistol and attached it to her belt. "Okay, EDI. What do I do?"

If the AI was happy with Traynor's acceptance of the situation, she didn't show it. "First, you need a way for us to stay in contact. Do you know if the Commander kept any personal communication devices."

Traynor wasn't sure. She started looking through drawers and compartments in searching. Most were empty, unsurprising given Shepard's mannerisms. In desperation, Traynor checked the closet.

What she found surprised her. Among four identical uniforms, a set of Dress Blues, and some civilian clothes, was a simple black dress. From the looks of it, it hadn't been worn much, and Samantha had never seen Shepard in it.

Traynor brushed aside the pain in her heart and kept searching. Finally, on the top shelf, she found what she was looking for: a box of simple military earbuds. She took one out and was about to sync it with her Omni-tool, when something caught her eye.

Next to the box... was an Omni-tool. Unlike her own, this one was covered in scratches, and was worn from use.

She realized it was Shepard's spare. She knew the Commander had two identical Omni-tools, just in case one was damaged during a mission. From the looks of it, she had switched between the two constantly.

Traynor stared at the battle-worn tool for a moment. Then, with a flick of her wrist, she took off her own Omni-tool and replaced it with Shepard's.

_Just in case,_ she thought to herself.

She synced the new Omni-tool to the comms desk, then synced the earbud with the Omni-tool. "Okay EDI. I'm ready."

"Good." The AI's voice sounded crisp and clear in Traynor's ear. "The nearest shaft to you is near the elevator. There will be a panel labeled was 'Maintenance Entrance.'"

Traynor exited the room, keeping her eyes ahead and her nose covered as she stepped through the mangled remains of her would be attackers. Sure enough, just over the railing, was the panel EDI had mentioned. She climbed over the railing, balancing on the pipes and conduits as she pried the panel open. The shaft inside stretched down the length of the ship. Of to the side was a shaft that went straight down, ladder rungs bolted into the sides of it.

Traynor took a deep breath and let it out slowly. There was no shake now.

"Okay," She said to herself. "Let's go save the ship."

* * *

**A/n: Sorry if it seemed like a long wait, but I just started back up into college, so updates might be few and far between. I'll try to make sure that it's worth the wait.**

**Remember, lengthy reviesw equal lengthy chapters!**


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